Organism : Bacillus cereus ATCC14579 | Module List :
BC4650

Transcriptional regulators, LysR family (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4650
(Mouseover regulator name to see its description)

BC4650 is regulated by 34 influences and regulates 27 modules.
Regulators for BC4650 (34)
Regulator Module Operator
BC0042 223 tf
BC1131 223 tf
BC1537 223 tf
BC1673 223 tf
BC1724 223 tf
BC1731 223 tf
BC1842 223 tf
BC2904 223 tf
BC3069 223 tf
BC3207 223 tf
BC3389 223 tf
BC3438 223 tf
BC3758 223 tf
BC4101 223 tf
BC4222 223 tf
BC4425 223 tf
BC4650 223 tf
BC5176 223 tf
BC5363 223 tf
BC5481 223 tf
BC0607 10 tf
BC2181 10 tf
BC2631 10 tf
BC2770 10 tf
BC2904 10 tf
BC3653 10 tf
BC3961 10 tf
BC4057 10 tf
BC4204 10 tf
BC4314 10 tf
BC4499 10 tf
BC4650 10 tf
BC5411 10 tf
BC5481 10 tf

Warning: BC4650 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
3942 1.90e+03 AaAgGa.G
Loader icon
3943 1.20e+04 gGTtcG.aTgCgA
Loader icon
4362 7.90e-05 AGAagaagagA
Loader icon
4363 2.50e+04 cCTGCTCaTGC
Loader icon
Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for BC4650

BC4650 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BC4650

BC4650 has total of 45 gene neighbors in modules 10, 223
Gene neighbors (45)
Gene Common Name Description Module membership
BC0303 BC0303 Alpha/beta hydrolase (NCBI ptt file) 10, 432
BC0389 BC0389 Spore coat protein B (NCBI ptt file) 223, 437
BC0416 BC0416 Phage infection protein (NCBI ptt file) 10, 461
BC0454 BC0454 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 10, 281
BC0610 BC0610 Magnesium and cobalt efflux protein corC (NCBI ptt file) 223, 437
BC0881 BC0881 Sensor protein comP (NCBI ptt file) 10, 85
BC0920 BC0920 hypothetical Cytosolic Protein (NCBI ptt file) 223, 404
BC1042 BC1042 hypothetical Cytosolic Protein (NCBI ptt file) 10, 256
BC1220 BC1220 hypothetical protein (NCBI ptt file) 26, 223
BC1455 BC1455 Multimodular transpeptidase-transglycosylase PBP 2A (NCBI ptt file) 223, 256
BC1561 BC1561 hypothetical Cytosolic Protein (NCBI ptt file) 10, 489
BC1574 BC1574 IAA acetyltransferase (NCBI ptt file) 223, 460
BC2063 BC2063 Alanine racemase (NCBI ptt file) 10, 223
BC2181 BC2181 Transcriptional regulator, Cro/CI family (NCBI ptt file) 10, 461
BC2321 BC2321 tRNA pseudouridine synthase A (NCBI ptt file) 10, 468
BC2427 BC2427 hypothetical protein (NCBI ptt file) 223, 255
BC2429 BC2429 ABC transporter ATP-binding protein (NCBI ptt file) 10, 276
BC2444 BC2444 Transcription state regulatory protein abrB (NCBI ptt file) 10, 308
BC2461 BC2461 Antigen (NCBI ptt file) 10, 174
BC2583 BC2583 Terminase large subunit (NCBI ptt file) 209, 223
BC2720 BC2720 Transporter (NCBI ptt file) 10, 276
BC2755 BC2755 Integral membrane protein (NCBI ptt file) 10, 148
BC2846 BC2846 Protein dltD precursor (NCBI ptt file) 159, 223
BC2862 BC2862 Protein export protein prsA precursor (NCBI ptt file) 10, 265
BC2895 BC2895 hypothetical protein (NCBI ptt file) 10, 55
BC3110 BC3110 Spore germination protein BC (NCBI ptt file) 10, 256
BC3300 BC3300 hypothetical protein (NCBI ptt file) 10, 404
BC3337 BC3337 Acetyltransferase (NCBI ptt file) 202, 223
BC3427 BC3427 Glycosyltransferase (NCBI ptt file) 202, 223
BC3430 BC3430 hypothetical protein (NCBI ptt file) 223, 254
BC3496 BC3496 None 223, 347
BC4186 BC4186 Stage III sporulation protein AH (NCBI ptt file) 10, 346
BC4205 BC4205 Spore photoproduct lyase (NCBI ptt file) 223, 369
BC4319 BC4319 Spore protease (NCBI ptt file) 202, 223
BC4372 BC4372 Penicillin-binding protein (NCBI ptt file) 223, 404
BC4541 BC4541 Methyltransferase (NCBI ptt file) 10, 265
BC4650 BC4650 Transcriptional regulators, LysR family (NCBI ptt file) 10, 223
BC4733 BC4733 Spore germination protein IC (NCBI ptt file) 205, 223
BC4771 BC4771 Sporulation kinase (NCBI ptt file) 60, 223
BC4820 BC4820 hypothetical protein (NCBI ptt file) 172, 223
BC4821 BC4821 hypothetical protein (NCBI ptt file) 172, 223
BC4939 BC4939 Stage 0 sporulation regulatory protein (NCBI ptt file) 10, 62
BC5202 BC5202 UDP-glucose 6-dehydrogenase (NCBI ptt file) 202, 223
BC5412 BC5412 Two-component sensor protein yhcY (NCBI ptt file) 202, 223
BC5425 BC5425 Integral membrane protein (NCBI ptt file) 10, 341
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for BC4650
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend